data_3U3J # _model_server_result.job_id 2uGEtBAQJB3Q-d5vwf3W7g _model_server_result.datetime_utc '2024-11-26 10:06:48' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3u3j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2001}' # _entry.id 3U3J # _exptl.entry_id 3U3J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3U3J _cell.length_a 72.097 _cell.length_b 79.422 _cell.length_c 121.807 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U3J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 3U3J _atom_sites.fract_transf_matrix[1][1] 0.01387 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012591 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.00821 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 A3P A 1 2001 2001 A3P A3P . D 2 A3P B 1 2001 2001 A3P A3P . E 3 HOH A 1 295 3 HOH HOH . E 3 HOH A 2 296 5 HOH HOH . E 3 HOH A 3 297 6 HOH HOH . E 3 HOH A 4 298 19 HOH HOH . E 3 HOH A 5 299 32 HOH HOH . E 3 HOH A 6 300 36 HOH HOH . E 3 HOH A 7 301 41 HOH HOH . E 3 HOH A 8 302 42 HOH HOH . E 3 HOH A 9 303 43 HOH HOH . E 3 HOH A 10 304 51 HOH HOH . F 3 HOH B 1 295 14 HOH HOH . F 3 HOH B 2 296 15 HOH HOH . F 3 HOH B 3 297 16 HOH HOH . F 3 HOH B 4 298 25 HOH HOH . F 3 HOH B 5 299 26 HOH HOH . F 3 HOH B 6 300 28 HOH HOH . F 3 HOH B 7 301 37 HOH HOH . F 3 HOH B 8 302 38 HOH HOH . F 3 HOH B 9 303 40 HOH HOH . F 3 HOH B 10 304 46 HOH HOH . F 3 HOH B 11 305 53 HOH HOH . F 3 HOH B 12 306 54 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P P1 A3P . . . D 2 -19.717 40.154 3.086 1 33.37 ? P1 A3P 2001 B 1 HETATM 2 O O1P A3P . . . D 2 -18.767 40.392 4.236 1 29.55 ? O1P A3P 2001 B 1 HETATM 3 O O2P A3P . . . D 2 -20.682 39 3.216 1 32.56 ? O2P A3P 2001 B 1 HETATM 4 O O3P A3P . . . D 2 -20.369 41.432 2.616 1 32.44 ? O3P A3P 2001 B 1 HETATM 5 P P2 A3P . . . D 2 -16.719 40.787 -3.739 1 31.33 ? P2 A3P 2001 B 1 HETATM 6 O O4P A3P . . . D 2 -17.452 42.078 -4.069 1 28.23 ? O4P A3P 2001 B 1 HETATM 7 O O5P A3P . . . D 2 -15.23 40.997 -3.489 1 32.39 ? O5P A3P 2001 B 1 HETATM 8 O O6P A3P . . . D 2 -17.007 39.521 -4.542 1 27.91 ? O6P A3P 2001 B 1 HETATM 9 O O5' A3P . . . D 2 -17.413 40.346 -2.378 1 31.39 ? O5' A3P 2001 B 1 HETATM 10 C C5' A3P . . . D 2 -16.981 40.844 -1.134 1 32.98 ? C5' A3P 2001 B 1 HETATM 11 C C4' A3P . . . D 2 -17.524 39.89 -0.098 1 34.74 ? C4' A3P 2001 B 1 HETATM 12 O O4' A3P . . . D 2 -16.507 38.95 0.272 1 35.59 ? O4' A3P 2001 B 1 HETATM 13 C C3' A3P . . . D 2 -17.945 40.582 1.184 1 35.59 ? C3' A3P 2001 B 1 HETATM 14 O O3' A3P . . . D 2 -18.774 39.666 1.909 1 33.58 ? O3' A3P 2001 B 1 HETATM 15 C C2' A3P . . . D 2 -16.629 40.713 1.883 1 37 ? C2' A3P 2001 B 1 HETATM 16 O O2' A3P . . . D 2 -16.746 41.031 3.28 1 38.67 ? O2' A3P 2001 B 1 HETATM 17 C C1' A3P . . . D 2 -16.089 39.299 1.603 1 37.49 ? C1' A3P 2001 B 1 HETATM 18 N N9 A3P . . . D 2 -14.616 39.259 1.719 1 38.27 ? N9 A3P 2001 B 1 HETATM 19 C C8 A3P . . . D 2 -13.737 40.115 1.168 1 38.04 ? C8 A3P 2001 B 1 HETATM 20 N N7 A3P . . . D 2 -12.496 39.727 1.514 1 37.77 ? N7 A3P 2001 B 1 HETATM 21 C C5 A3P . . . D 2 -12.612 38.629 2.271 1 38.58 ? C5 A3P 2001 B 1 HETATM 22 C C6 A3P . . . D 2 -11.682 37.827 2.896 1 40.36 ? C6 A3P 2001 B 1 HETATM 23 N N6 A3P . . . D 2 -10.351 38.084 2.784 1 41.24 ? N6 A3P 2001 B 1 HETATM 24 N N1 A3P . . . D 2 -12.137 36.777 3.611 1 42.03 ? N1 A3P 2001 B 1 HETATM 25 C C2 A3P . . . D 2 -13.466 36.519 3.713 1 42.08 ? C2 A3P 2001 B 1 HETATM 26 N N3 A3P . . . D 2 -14.38 37.287 3.11 1 39.59 ? N3 A3P 2001 B 1 HETATM 27 C C4 A3P . . . D 2 -13.956 38.338 2.391 1 37.81 ? C4 A3P 2001 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #